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Article ; Online: M7G methylated core genes (METTL1 and WDR4) and associated RNA risk signatures are associated with prognosis and immune escape in HCC.

Li, Rui / Liu, Xincheng / Deng, Kaiyuan / Wang, Xin

2023 Volume 16, Issue 1, Page(s) 179

Abstract: N7 methylguanosine (m7G) has a crucial role the development of hepatocellular carcinoma (HCC). This study aimed to investigate the impact of the m7G methylation core genes (METTL1 and WDR4) and associated RNA risk signatures on HCC. we found m7G ... ...

Abstract	N7 methylguanosine (m7G) has a crucial role the development of hepatocellular carcinoma (HCC). This study aimed to investigate the impact of the m7G methylation core genes (METTL1 and WDR4) and associated RNA risk signatures on HCC. we found m7G methylation core genes (METTL1 and WDR4) were upregulated in four HCC cell lines, and downregulation of METTL1 and WDR4 attenuated HCC cell proliferation, migration, and invasion. Moreover, METTL1 and WDR4 are upregulated in HCC tissues, and that there is a significant positive correlation between them. METTL1 and WDR4 were identified as independent prognostic markers for HCC by employing overall survival (OS), disease-specific survival (DSS), Progression Free Interval survival (PFI), and univariate/multivariate Cox analyses. We identified 1479 coding RNAs (mRNAs) and 232 long non-coding RNAs (lncRNAs) associated with METTL1 / WDR4 by using weighted coexpression network analysis (WGCNA) and co-clustering analysis. The least absolute shrinkage and selection operator (lasso) were used to constructing mRNA and lncRNA risk signatures associated with the METTL1 / WDR4. These risk were independent poor prognostic factors in HCC. Furthermore, we found that METTL1 / WDR4 expression and mRNA / lncRNA risk scores were closely associated with TP53 mutations. Clinicopathological features correlation results showed that METTL1 / WDR4 expression and mRNA / lncRNA risk score were associated with the stage and invasion depth (T) of HCC. To predict the overall survival of HCC individuals, we constructed a nomogram with METTL1/WDR4 expression, mRNA/lncRNA risk score, and clinicopathological features. In addition, we combined single-cell sequencing datasets and immune escape-related checkpoints to construct an immune escape-related protein-protein interaction(PPI) network. In conclusion, M7G methylated core genes (METTL1 and WDR4) and associated RNA risk signatures are associated with prognosis and immune escape in HCC.
MeSH term(s)	Humans ; Carcinoma, Hepatocellular/genetics ; RNA, Long Noncoding/genetics ; Liver Neoplasms/genetics ; Prognosis ; Cell Line ; GTP-Binding Proteins ; Methyltransferases/genetics
Chemical Substances	RNA, Long Noncoding ; WDR4 protein, human ; GTP-Binding Proteins (EC 3.6.1.-) ; METTL1 protein, human (EC 2.1.1.-) ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2023-08-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-023-01614-8
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Article ; Online: TOR1AIP1

Mackels, Laurane / Liu, Xincheng / Bonne, Gisèle / Servais, Laurent

International journal of molecular sciences

2023 Volume 24, Issue 8

Abstract: ... ...

Abstract	Human
MeSH term(s)	Humans ; Membrane Proteins/metabolism ; Muscular Dystrophies/metabolism ; Mutation ; Nuclear Envelope/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Cytoskeletal Proteins/metabolism
Chemical Substances	Membrane Proteins ; Nuclear Proteins ; TOR1AIP1 protein, human ; Cytoskeletal Proteins
Language	English
Publishing date	2023-04-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24086911
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Article ; Online: Screening of different flours for 3D food printing: Optimization of thermomechanical process of soy and rye flour dough

Guénard-Lampron, Valérie / Liu, Xincheng / Masson, Marine / Blumenthal, David

Innovative Food Science and Emerging Technologies. 2023 July, v. 87 p.103394-

2023

Abstract: 3D food printing allows the development of personalized food, but it is necessary to diversify the printable recipes to propose a varied food offer. The objective of this project was to explore the printability potential of different flours and to ... ...

Abstract	3D food printing allows the development of personalized food, but it is necessary to diversify the printable recipes to propose a varied food offer. The objective of this project was to explore the printability potential of different flours and to optimize a thermomechanical process (mixing and heating of water and flour) to ensure good print quality. A bibliographic study of 25 flours and an experimental screening of five flours was conducted. Thanks to the previous steps, soy and rye flour were selected because of their interesting nutritional value and their printability potential. An experimental design (10 trials) for each flour showed a significant impact of the process parameters studied (percentage of water content and duration of the thermomechanical treatment) on print quality. The reverse engineering approach demonstrated that the optimal water content is similar for both flour (Soy: 59%, Rye: 60%), but the optimal duration of the thermomechanical treatment is quite different (Soy: 27 min, Rye: 22 min). Interest in 3D food printing has continued to grow in recent years. Products with different flavors, shapes and textures have been proposed in many studies. However, print quality is not always easy to predict and to obtain, especially when faced with nutritional or functional constraints. In our study, we developed a 3-steps approach (two screening steps including bibliographic and experimental method and then one optimization step) to propose new edible ink combining interesting nutritional composition and good print quality. To achieve this goal a design of experiments based on two process parameters (water content and duration of thermomechanical treatment) was conducted and a predictive model was established for soy and rye flours. The reverse-engineering method allowed determining the process parameters to use to ensure good print quality and stability of 3D-printed products. This approach could be applied for the development of new edible ink using other flours or integrating different ingredients.
Keywords	dough ; experimental design ; models ; nutrient content ; nutritive value ; rye ; rye flour ; water content ; 3D food printing ; Food processing ; Desirability function ; Reverse engineering
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	2025029-0
ISSN	1466-8564
ISSN	1466-8564
DOI	10.1016/j.ifset.2023.103394
Database	NAL-Catalogue (AGRICOLA)

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Article: Machine learning and experiments revealed a novel pyroptosis-based classification linked to diagnosis and immune landscape in spinal cord injury.

Zhang, Zhao / Zhu, Zhijie / Liu, Dong / Wang, Xuankang / Liu, Xincheng / Mi, Zhenzhou / Fu, Jun / Fan, Hongbin

Heliyon

2024 Volume 10, Issue 3, Page(s) e24974

Abstract: Background: Rising evidence indicates the development of pyroptosis in the initiation and pathogenesis of spinal cord injury (SCI). However, the associated effects of pyroptosis-related genes (PRGs) in SCI are unclear.: Methods: We obtained the gene ... ...

Abstract	Background: Rising evidence indicates the development of pyroptosis in the initiation and pathogenesis of spinal cord injury (SCI). However, the associated effects of pyroptosis-related genes (PRGs) in SCI are unclear. Methods: We obtained the gene expression profiles of SCI and normal samples in the GEO. Database: The R package limma screened for differentially expressed (DE) PRGs and performed functional enrichment analysis. Mechanical learning and PPI analysis helped filter essential PRGs to diagnose SCI. Peripheral blood was collected for validation from ten SCI patients and eight healthy individuals. The association of essential PRGs with immune infiltration was evaluated, and pyroptosis subtypes were recognized in SCI patients by unsupervised cluster analysis. Besides, a SCI model was built for in vivo validation of essential PRGs. Result: We identified 25 DE-PRGs between SCI and normal controls. Functional enrichment analysis revealed the principal involvement of DE-PRGs in pyroptosis, inflammasome complex, interleukin-1 beta production, etc. Subsequently, three essential PRGs were identified and validated, showing excellent diagnostic efficacy and significant correlation with immune cell infiltration. Additionally, we developed diagnostic nomograms to predict the occurrence of SCI. Two pyroptosis subtypes exhibited distinct biological functions and immune landscapes among SCI patients. Finally, the expression of these essential PRGswas verified in vivo. Conclusion: The current study described the vital effects of pyroptosis-related genes in SCI, providing a novel direction for effective assessment and management of SCI.
Language	English
Publishing date	2024-01-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e24974
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Article ; Online: Analysis of polyhalogenated carbazoles and two related compounds in earthworms using a modified QuEChERS method with GC/MS and GC/MS/MS.

Li, Chaojie / Su, Qi / Wu, Juan / Zhou, Xinmei / Zhong, Dan / Liu, Xincheng / Zhou, Shanshan

Environmental science and pollution research international

2023 Volume 30, Issue 36, Page(s) 86255–86267

Abstract: A precise analytical method based on QuEChERS has been proposed for the concurrent determination of 11 polyhalogenated carbazoles (PHCZs), benzocarbazole (BZCZ), and 9H-carbazoles (CZ). The quantification was confirmed by gas chromatography using triple ... ...

Abstract	A precise analytical method based on QuEChERS has been proposed for the concurrent determination of 11 polyhalogenated carbazoles (PHCZs), benzocarbazole (BZCZ), and 9H-carbazoles (CZ). The quantification was confirmed by gas chromatography using triple quadrupole tandem mass spectrometry (Shimadzu GC-MS/MS-TQ8040) and gas chromatography coupled mass spectrometry (Agilent 7890A-5973 GC-MS). The developed method was validated by testing the following parameters: linearity, instrument limit of detection (LOD), instrument limit of quantification (LOQ), method limit of detection (MLD), method limit of quantification (MLQ), matrix effect (ME), accuracy, and precision. All compounds showed good linearity in the range of 0.005-0.2 μg/mL with correlation coefficients higher than 0.992. The method demonstrated satisfactory recoveries (ranging from 71.21 to 105.04%) for most of the compounds with relative standard deviation precision (RSD) < 10.46%, except 3-BCZ (Recovery = 67.53%, RSD = 2.83%). The values of LOD and LOQ varied from 0.05 to 0.24 ng and 0.14 to 0.92 ng, respectively, while those of MLD and MLQ ranged from 0.02 to 0.12 ng/g wet weight (ww) and 0.07 to 0.45 ng/g ww, respectively. The developed method represents a reliable tool for the routine analysis of PHCZ congeners in invertebrate animals.
MeSH term(s)	Animals ; Gas Chromatography-Mass Spectrometry/methods ; Tandem Mass Spectrometry/methods ; Oligochaeta ; Limit of Detection ; Carbazoles/analysis
Chemical Substances	Carbazoles
Language	English
Publishing date	2023-07-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-023-28535-4
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Article ; Online: Development and experimental validation of a folate metabolism-related gene signature to predict the prognosis and immunotherapeutic sensitivity in bladder cancer.

Liu, Xincheng / Chen, Chunxiao / Xu, Peng / Chen, Binshen / Xu, Abai / Liu, Chunxiao

Functional & integrative genomics

2023 Volume 23, Issue 4, Page(s) 291

Abstract: Folate metabolism is critical for the maintenance of genomic stability due to its regulatory ability to methylation, nucleotide metabolism, and reduction capabilities in cancer cells. However, the prognostic value of folate metabolism-related genes has ... ...

Abstract	Folate metabolism is critical for the maintenance of genomic stability due to its regulatory ability to methylation, nucleotide metabolism, and reduction capabilities in cancer cells. However, the prognostic value of folate metabolism-related genes has not been clarified, especially in bladder cancer (BLCA). 91 folate metabolism-related genes were retrieved from the public database. TCGA-BLCA cohort, obtained from the Cancer Genome Atlas, was selected for training, while GSE13507, GSE31684, and GSE32894, downloaded from the Gene Expression Omnibus, and 35 BLCA samples collected from the local hospital were used for external validation. Through genomic difference detection, protein-protein interaction network analysis, LASSO regression, and Cox regression, a three-gene signature, including ATIC, INS, and MTHFD1L, was constructed. The signature was a reliable prognosis predictor across multiple independent cohorts (pooled hazard ratio = 2.79, 95% confidence interval = 1.79-4.33). The signature was associated with the BLCA malignant degree, which was validated in the local clinical samples (P < 0.01) and multiple cell lines (all P < 0.05). Additionally, the TIDE algorithm, GSE111636 cohort, and IMvigor210 cohort indicated that the signature was a promising tool to evaluate the immunotherapeutic response. Collectively, a folate metabolism-related gene signature was constructed to predict the prognosis and immunotherapeutic sensitivity in BLCA, which was verified in multiple large-scale cohorts, clinical samples, and cellular experiments, providing novel insights into the biological mechanisms.
MeSH term(s)	Humans ; Urinary Bladder Neoplasms/genetics ; Urinary Bladder Neoplasms/therapy ; Algorithms ; Cell Line ; Immunotherapy ; Folic Acid
Chemical Substances	Folic Acid (935E97BOY8)
Language	English
Publishing date	2023-09-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2014670-X
ISSN	1438-7948 ; 1438-793X
ISSN (online)	1438-7948
ISSN	1438-793X
DOI	10.1007/s10142-023-01205-x
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Article ; Online: Anoikis patterns exhibit distinct prognostic and immune landscapes in Osteosarcoma.

Zhang, Zhao / Zhu, Zhijie / Fu, Jun / Liu, Xincheng / Mi, Zhenzhou / Tao, Huiren / Fan, Hongbin

International immunopharmacology

2023 Volume 115, Page(s) 109684

Abstract: Objectives: Osteosarcoma is highly aggressive and prone to metastasis, with a poor prognosis. Increasing evidence identified anoikis has a critical effect in tumor metastasis and invasion. However, the prognostic value of anoikis-related genes (ANRGs) ... ...

Abstract	Objectives: Osteosarcoma is highly aggressive and prone to metastasis, with a poor prognosis. Increasing evidence identified anoikis has a critical effect in tumor metastasis and invasion. However, the prognostic value of anoikis-related genes (ANRGs) in osteosarcoma and their role in the immune landscape of osteosarcoma remain unclear. Methods: The RNA sequencing and clinical data of patients with osteosarcoma were extracted from the TARGET and GEO databases, and ANRGs were identified from the GeneCards database. Unsupervised clustering analysis was employed to identify anoikis-related patterns. The ESTIMATE, TIMER and ssGSEA algorithms were used to assess the immune microenvironment of different subtypes. A prognostic signature based on the identified ANRGs was constructed via univariate, LASSO and multivariate Cox regression analyses. KEGG, GO and GSEA were used for functional enrichment of genes associated with different risk subtypes. qPCR, WB and IHC were used to validate the expression of candidate genes. Results: Two anoikis-related patterns with distinct clinical features and immune statuses were identified based on prognosis-related ANRGs. Cluster 2 had more active immunogenicity and a better prognosis than Cluster 1. Subsequently, we developed and validated an anoikis prognostic signature demonstrating excellent predictive ability for the prognosis of osteosarcoma. Anoikis risk score was positively associated with osteosarcoma metastasis and was identified as an independent prognostic marker. Additionally, a nomogram was established to predict the 3- and 5-year survival probability of patients with osteosarcoma. Functional enrichment analysis revealed that immune dysregulation was correlated with poor prognosis. Besides, patients in the low-risk group had higher infiltration levels of immune cells and more active immune function than patients in the high-risk group. Drug sensitivity analysis revealed several chemotherapeutic agents for the treatment of different subtypes of osteosarcoma. Conclusion: Our study demonstrated the role of ANRGs in osteosarcoma progression, providing insights into clinical decision making in osteosarcoma.
MeSH term(s)	Humans ; Prognosis ; Anoikis/genetics ; Nomograms ; Osteosarcoma/genetics ; Bone Neoplasms/genetics ; Tumor Microenvironment
Language	English
Publishing date	2023-01-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2043785-7
ISSN	1878-1705 ; 1567-5769
ISSN (online)	1878-1705
ISSN	1567-5769
DOI	10.1016/j.intimp.2023.109684
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Article ; Online: Gasless Single-Incision Endoscopic Surgery via Subclavicular Approach for Lateral Neck Dissection in Patients with Papillary Thyroid Cancer.

Zheng, Guibin / Ding, Weifang / Liu, Xincheng / Liu, Yang / Sun, Haiqing / Song, Xicheng / Zheng, Haitao

Annals of surgical oncology

2023 Volume 31, Issue 3, Page(s) 1498–1508

Abstract: Background: The technical difficulties and trauma of remote access methods in endoscopic surgery (ES) for lateral neck dissection (LND) can be daunting for most patients with papillary thyroid cancer (PTC) and surgeons. The purpose of study was to ... ...

Abstract	Background: The technical difficulties and trauma of remote access methods in endoscopic surgery (ES) for lateral neck dissection (LND) can be daunting for most patients with papillary thyroid cancer (PTC) and surgeons. The purpose of study was to introduce gasless single-incision ES via a subclavicular approach (ESSA) and to explore its safety and efficacy for LND. Methods: Between January 2022 and February 2023, we retrospectively reviewed 17 patients with PTC who underwent ESSA for LND. In addition, 22 patients who received video-assisted ES (VAES) and 48 patients who underwent open surgery (OP) for LND during the same period were included. Clinicopathological characteristics, complications, and efficacy of the lymph node yield (LNY) were compared between the ESSA and the other two groups (VAES and OP). Results: The LNY from central and lateral neck dissection by ESSA was comparable to that by VAES (9.2 ± 8.1 vs. 9.5 ± 4.2, P = 0.986, and 33.5 ± 11.6 vs. 30.6 ± 9.2, P = 0.382, respectively) and OP (9.2 ± 8.1 vs. 11.0 ± 5.4, P = 0.420, and 33.5 ± 11.6 vs. 31.5 ± 7.9, P = 0.383, respectively). Swallowing impairment scores at 1 and 3 months were significantly lower after ESSA than those after VAES (1.8 ± 1.0 vs. 3.0 ± 1.2, P = 0.003, and 0.9 ± 0.8 vs. 1.7 ± 0.8, P = 0.006, respectively). The cosmetic satisfaction rate 1 month after surgery was significantly higher in the ESSA group than that in the VAES group (100 vs. 31.8%, P < 0.001). Conclusions: ESSA is a safe and minimally invasive procedure that provides a scarless cervical appearance and has good efficacy for LND. Therefore, ESSA may be a feasible choice for selected patients with N1b PTC with cervical cosmetic needs.
MeSH term(s)	Humans ; Neck Dissection/methods ; Thyroid Cancer, Papillary/surgery ; Thyroid Neoplasms/surgery ; Thyroidectomy/methods ; Retrospective Studies ; Carcinoma, Papillary/surgery ; Surgical Wound/surgery
Language	English
Publishing date	2023-12-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1200469-8
ISSN	1534-4681 ; 1068-9265
ISSN (online)	1534-4681
ISSN	1068-9265
DOI	10.1245/s10434-023-14639-1
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Article: Probing the generation mechanism of emulsion based on shearing actions between multiphase fluids in porous media

Wang, Zhe / Cao, Guangsheng / Bai, Yujie / Wang, Peilun / Liu, Xincheng / Wang, Xin

Colloids and surfaces. 2022 Nov. 20, v. 653

2022

Abstract: The generation, migration, and coalescence processes of emulsions in porous media of the actual formations are relatively complex. However, few studies have been reported about the generation mechanism of emulsions under shearing action, especially under ...

Abstract	The generation, migration, and coalescence processes of emulsions in porous media of the actual formations are relatively complex. However, few studies have been reported about the generation mechanism of emulsions under shearing action, especially under shearing action between multiphase fluids. In this paper, the concept of emulsification caused by fluid shearing was proposed for the first time. An oil-water two phases flow model in porous media was established to study the generation process of emulsion caused by shearing actions between oil and water. Fluid flow velocity, pressure and distribution characteristics of oil and water during this process were recorded. The effects of flow velocity and oil-water interface properties on the generation process of emulsion were investigated. Combined with the microscopic visualization oil displacement model, the generation characteristics of emulsions in porous media were further explored. The results indicated that the complex flow between oil and water in porous media would cause shear emulsification of crude oil. With the increase of flow velocity of oil-water two phases, the shear emulsification capacity was gradually enhanced. The generation capacity of emulsion in the micro shearing unit was mainly affected by the flow velocity of the displacing phase, and the particle size of the emulsion was mainly affected by the flow velocity of the shearing phase. When the interfacial tension between oil and water was lower than 10⁻¹ mN/m, the shear emulsification rate did not change significantly. These results are of great significance for the supplement and improvement of the generation mechanism of emulsions in porous media, providing theoretical guidance for further enhancing oil recovery by regulating emulsification.
Keywords	emulsifying ; emulsions ; models ; oil-water interface ; oils ; particle size ; petroleum ; surface tension
Language	English
Dates of publication	2022-1120
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1500517-3
ISSN	0927-7757
ISSN	0927-7757
DOI	10.1016/j.colsurfa.2022.129997
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Article: The pharmacological evidence of the chang-yan-ning formula in the treatment of colitis.

Yu, Wei / Zhang, Yijia / Kang, Cai / Zheng, Yang / Liu, Xincheng / Liang, Zhenghao / Yan, Jing

Frontiers in pharmacology

2022 Volume 13, Page(s) 1029088

Abstract: Ulcerative colitis (UC) is a subtype of inflammatory bowel disease (IBD) and occurs mainly in the colon. The etiology of UC is rather complex and involves various pathological factors, including genetic susceptibility, dietary intakes, environment, and ... ...

Abstract	Ulcerative colitis (UC) is a subtype of inflammatory bowel disease (IBD) and occurs mainly in the colon. The etiology of UC is rather complex and involves various pathological factors, including genetic susceptibility, dietary intakes, environment, and microbiota. In China, the Chang-Yan-Ning (CYN) formula has been utilized in the clinic to treat gastrointestinal disorders, but its pharmacological evidence remains elusive. The investigation was designed to explore the molecular and cellular mechanisms of CYN. Liquid Chromatography with tandem mass spectrometry (LC/MS) was performed to identify the key components in the formula; Network pharmacology analysis was executed to predict the potential targets of CYN; An experimental murine colitis model was established by utilizing 2% dextran sodium sulfate (DSS), and CYN was administered for 14 days. The pharmacological mechanism of the CYN formula was corroborated by
Language	English
Publishing date	2022-10-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2022.1029088
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